Istanbul Health and Technology University INFORMATION PACKAGE / COURSE CATALOGUE
| Molecular Biology and Genetics | |||||
| Bachelor | TR-NQF-HE: Level 6 | QF-EHEA: First Cycle | EQF-LLL: Level 6 | ||
Course General Introduction Information
| Course Code: | MBG309 | ||||
| Course Name: | Genome Databases and Bioinformatics Tools | ||||
| Course Semester: | Fall | ||||
| Course Credits: |
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| Language of instruction: | TR | ||||
| Course Requirement: | |||||
| Does the Course Require Work Experience?: | No | ||||
| Type of course: | Necessary | ||||
| Course Level: |
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| Mode of Delivery: | Face to face | ||||
| Course Coordinator : | Dr.Öğr.Üyesi SONER AKSU | ||||
| Course Lecturer(s): | Soner Aksu, PhD | ||||
| Course Assistants: |
Course Purpose and Content
| Course Objectives: | With this course, it is aimed to provide undergraduate students with the ability to access genetic data, to obtain the data needed, to use basic bioinformatics tools related to data search and processing, and to gain competence in the basic definitions and principles related to these research and analysis activities. The course will be carried out in a real-time applied manner in the computer laboratory, and students will be provided with experience by making one-to-one applications. In addition, theoretical information about the terms, terms and methods encountered will be given. Apart from the practical training in the lectures, the knowledge gained will be reinforced with homework assignments and these homework grades will constitute the second midterm grade. |
| Course Content: | 1. Scientific literature databases 2. Ensembl genome databank - access to basic genomic data 3. Ensembl and BLAST application 4. Ensembl and BioMart application 5. NCBI databank - access to basic genomic data 6. NCBI databank - GenBank and RefSeq 7. NCBI - Basic BLAST 8. NCBI - Map Viewer 9. UCSC genome databank - access to basic genomic data 10. Gene Ontology (GO) - Metabolic Pathway and Gene Function Database 11. Kyoto Encyclopedia (KEGG) - Gene and Genome Data Bank 12. Nucleotide sequence converters, Primer3: primer design, OligoCalc and AutoDimer: Primer quality control tools 13. Clustal Omega: DNA sequence alignment, Promotor region analysis |
Learning Outcomes
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The students who have succeeded in this course;
1) - Accessing basic data about a gene using genome databases: gene symbol, gene definition, genomic location, transcript variants and their differences, exon-intron, UTR information and DNA sequences, other genes with which they have paralogue and orthologous relationships, polymorphisms identified on the gene and their characteristics, structure and functions of the protein produced by the gene, metabolic pathways in which protein is involved, RefSeq mRNA sequence and protein sequence, 2) BLAST: definition, types, parameters and usage, 3) BioMart: description, use of filters, data scoping, utilisation, downloading and interpretation of data, 4) Gene Ontology (GO) and Kyoto Encyclopedia (KEGG): defining the functions of the protein produced by a gene and the metabolic pathways in which it participates, 5) Nucleotide Sequence Translators: Translation of DNA sequences supplied in a specific format into different formats, reverse, reverse-complement DNA sequence translations and nucleotide-amino acid sequence translations, 6) Primer3, OligoCalc, AutoDimer: primer design and quality control, 7) Clustal Omega: Alignment and comparison of DNA sequences, 8) Promotor Region Analysis: CpG island, TSS, First Exon, TF binding motifs and conserved sequence analyses pointing to the promoter region using different bioinformatics tools |
Course Flow Plan
| Week | Subject | Related Preparation |
| 1) | 1. Scientific literature databases 2. Ensembl genome databank - access to basic genomic data 3. Ensembl and BLAST application 4. Ensembl and BioMart application 5. NCBI databank - access to basic genomic data 6. NCBI databank - GenBank and RefSeq 7. NCBI - Basic BLAST 8. NCBI - Map Viewer 9. UCSC genome databank - access to basic genomic data 10. Gene Ontology (GO) - Metabolic Pathway and Gene Function Database 11. Kyoto Encyclopedia (KEGG) - Gene and Genome Data Bank 12. Nucleotide sequence converters, Primer3: primer design, OligoCalc and AutoDimer: Primer quality control tools 13. Clustal Omega: DNA sequence alignment, Promotor region analysis | Course Guides Presentations Lecture Notes |
Sources
| Course Notes / Textbooks: | Genom veri bankalarına ait web sayfaları Ders notları ve uygulamalar |
| References: | Web pages of genome databases Lecture notes and applications |
Course - Learning Outcome Relationship
| No Effect | 1 Lowest | 2 Medium | 3 Highest |
| Program Outcomes | Level of Contribution | |
| 1) | Having knowledge and understanding of Molecular Biology and Genetics subjects, established on competencies gained in previous education and supported by using course books containing latest information, application tools and other scientific literature. | 3 |
| 2) | Students can integrate knowledge and skills from molecular biology and genetics courses and can acquire further knowledge according to their own interests. | 3 |
| 3) | Students acquire practical skills in fundamental molecular biology and genetics techniques. | 3 |
| 4) | Ability of proposing solutions in unexpected, complicated situations on applications of Molecular Biology and Genetics by claiming responsibility individually or as a part of a team. | 1 |
| 5) | Competency in planning academic studies on Molecular Biology and Genetics and carrying out these studies individually or collectively. | 2 |
| 6) | Students can develop ability to analyse and interpret experimental data obtained in a laboratory setting statistically. | 1 |
| 7) | Sufficient foreign language knowledge for communication between colleagues and following literature on Molecular Biology and Genetics. | 2 |
| 8) | Students can use computational technologies to analyse scientific data and for information retrieval. | 3 |
| 9) | Being aware of the necessity of lifelong education, reaching information, following the advances in science and technology and constant struggle of renewing oneself. | 2 |
| 10) | Evaluating natural and social events with an environmental point of view and ability of informing and leading the public opinion | |
| 11) | Students acquire professional knowledge and skills to fulfil requirements of their future employers. | 3 |
| 12) | Having proper social, ethical and scientific values and the will to protect these values on studies about collection, evaluation, contemplation, publication and application of data regarding Molecular Biology and Genetics. | 1 |
| 13) | Students can understand and evaluate advantages and limitations of technological platforms in life sciences including genomics, genetic engineering and biotechnology. | 3 |
| 14) | Students would have consciousness on subjects such as the quality management, worker welfare and safety. |
Learning Activity and Teaching Methods
| Anlatım | |
| Bireysel çalışma ve ödevi | |
| Course | |
| Homework | |
| Uygulama (Modelleme, Tasarım, Maket, Simülasyon, Deney vs.) | |
| Web Tabanlı Öğrenme |
Measurement and Evaluation Methods and Criteria
| Yazılı Sınav (Açık uçlu sorular, çoktan seçmeli, doğru yanlış, eşleştirme, boşluk doldurma, sıralama) | |
| Sözlü sınav | |
| Homework | |
| Uygulama | |
| Bilgisayar Destekli Sunum |
Assessment & Grading
| Semester Requirements | Number of Activities | Level of Contribution |
| Homework Assignments | 4 | % 30 |
| Midterms | 1 | % 20 |
| Final | 1 | % 50 |
| total | % 100 | |
| PERCENTAGE OF SEMESTER WORK | % 50 | |
| PERCENTAGE OF FINAL WORK | % 50 | |
| total | % 100 | |
İş Yükü ve AKTS Kredisi Hesaplaması
| Activities | Number of Activities | Aktiviteye Hazırlık | Aktivitede Harçanan Süre | Aktivite Gereksinimi İçin Süre | Workload | ||
| Course Hours | 14 | 3 | 42 | ||||
| Application | 7 | 7 | 49 | ||||
| Study Hours Out of Class | 10 | 5 | 50 | ||||
| Homework Assignments | 4 | 1 | 4 | ||||
| Midterms | 1 | 1.5 | 1.5 | ||||
| Final | 1 | 1.5 | 1.5 | ||||
| Total Workload | 148 | ||||||